library(gridExtra)
library(knitr)
library(ggplot2)
library(fastqcr)
#must run this if fastqc is not already installed locally
#fastqc_install()
###ONLY THIS CHUNK REQUIRES MODIFICATION###
###assign your directory locations here:
#specify full path to directory containing a .fastq.gz file for each sample
fq.dir<-"/home/d669d153/work/phil.dicaeum/fastq"
#specify full path to the output directory where you want
qc.dir<-"/home/d669d153/work/phil.dicaeum/qc"
#run fastqc on all .fastq.gz files, through r
#This only needs to be run once, if only tweaking downstream visualizations, you can comment out this step
fastqc(fq.dir = fq.dir, # FASTQ files directory
qc.dir = qc.dir, # Results directory
threads = 4 # Number of threads
)
# List of files in the output directory to ensure fastqc worked
list.files(qc.dir)
[1] “D_hypoleucum_1271_fastqc.html”
[2] “D_hypoleucum_1271_fastqc.zip”
[3] “D_hypoleucum_1273_fastqc.html”
[4] “D_hypoleucum_1273_fastqc.zip”
[5] “D_hypoleucum_1275_fastqc.html”
[6] “D_hypoleucum_1275_fastqc.zip”
[7] “D_hypoleucum_14037_fastqc.html”
[8] “D_hypoleucum_14037_fastqc.zip”
[9] “D_hypoleucum_14061_fastqc.html”
[10] “D_hypoleucum_14061_fastqc.zip”
[11] “D_hypoleucum_14065_fastqc.html”
[12] “D_hypoleucum_14065_fastqc.zip”
[13] “D_hypoleucum_14075_fastqc.html”
[14] “D_hypoleucum_14075_fastqc.zip”
[15] “D_hypoleucum_14079_fastqc.html”
[16] “D_hypoleucum_14079_fastqc.zip”
[17] “D_hypoleucum_14120_fastqc.html”
[18] “D_hypoleucum_14120_fastqc.zip”
[19] “D_hypoleucum_14146_fastqc.html”
[20] “D_hypoleucum_14146_fastqc.zip”
[21] “D_hypoleucum_14181_fastqc.html”
[22] “D_hypoleucum_14181_fastqc.zip”
[23] “D_hypoleucum_14225_fastqc.html”
[24] “D_hypoleucum_14225_fastqc.zip”
[25] “D_hypoleucum_17969_fastqc.html”
[26] “D_hypoleucum_17969_fastqc.zip”
[27] “D_hypoleucum_17976_fastqc.html”
[28] “D_hypoleucum_17976_fastqc.zip”
[29] “D_hypoleucum_18070_fastqc.html”
[30] “D_hypoleucum_18070_fastqc.zip”
[31] “D_hypoleucum_18159_fastqc.html”
[32] “D_hypoleucum_18159_fastqc.zip”
[33] “D_hypoleucum_18188_fastqc.html”
[34] “D_hypoleucum_18188_fastqc.zip”
[35] “D_hypoleucum_18191_fastqc.html”
[36] “D_hypoleucum_18191_fastqc.zip”
[37] “D_hypoleucum_18193_fastqc.html”
[38] “D_hypoleucum_18193_fastqc.zip”
[39] “D_hypoleucum_19046_fastqc.html”
[40] “D_hypoleucum_19046_fastqc.zip”
[41] “D_hypoleucum_19066_fastqc.html”
[42] “D_hypoleucum_19066_fastqc.zip”
[43] “D_hypoleucum_19136_fastqc.html”
[44] “D_hypoleucum_19136_fastqc.zip”
[45] “D_hypoleucum_19177_fastqc.html”
[46] “D_hypoleucum_19177_fastqc.zip”
[47] “D_hypoleucum_19178_fastqc.html”
[48] “D_hypoleucum_19178_fastqc.zip”
[49] “D_hypoleucum_1956_fastqc.html”
[50] “D_hypoleucum_1956_fastqc.zip”
[51] “D_hypoleucum_19638_fastqc.html”
[52] “D_hypoleucum_19638_fastqc.zip”
[53] “D_hypoleucum_20193_fastqc.html”
[54] “D_hypoleucum_20193_fastqc.zip”
[55] “D_hypoleucum_20213_fastqc.html”
[56] “D_hypoleucum_20213_fastqc.zip”
[57] “D_hypoleucum_20214_fastqc.html”
[58] “D_hypoleucum_20214_fastqc.zip”
[59] “D_hypoleucum_20218_fastqc.html”
[60] “D_hypoleucum_20218_fastqc.zip”
[61] “D_hypoleucum_2067_fastqc.html”
[62] “D_hypoleucum_2067_fastqc.zip”
[63] “D_hypoleucum_20921_fastqc.html”
[64] “D_hypoleucum_20921_fastqc.zip”
[65] “D_hypoleucum_2208_fastqc.html”
[66] “D_hypoleucum_2208_fastqc.zip”
[67] “D_hypoleucum_2229_fastqc.html”
[68] “D_hypoleucum_2229_fastqc.zip”
[69] “D_hypoleucum_2253_fastqc.html”
[70] “D_hypoleucum_2253_fastqc.zip”
[71] “D_hypoleucum_25622_fastqc.html”
[72] “D_hypoleucum_25622_fastqc.zip”
[73] “D_hypoleucum_25637_fastqc.html”
[74] “D_hypoleucum_25637_fastqc.zip”
[75] “D_hypoleucum_25670_fastqc.html”
[76] “D_hypoleucum_25670_fastqc.zip”
[77] “D_hypoleucum_25672_fastqc.html”
[78] “D_hypoleucum_25672_fastqc.zip”
[79] “D_hypoleucum_25675_fastqc.html”
[80] “D_hypoleucum_25675_fastqc.zip”
[81] “D_hypoleucum_25868_fastqc.html”
[82] “D_hypoleucum_25868_fastqc.zip”
[83] “D_hypoleucum_25880_fastqc.html”
[84] “D_hypoleucum_25880_fastqc.zip”
[85] “D_hypoleucum_25921_fastqc.html”
[86] “D_hypoleucum_25921_fastqc.zip”
[87] “D_hypoleucum_26975_fastqc.html”
[88] “D_hypoleucum_26975_fastqc.zip”
[89] “D_hypoleucum_26984_fastqc.html”
[90] “D_hypoleucum_26984_fastqc.zip”
[91] “D_hypoleucum_27182_fastqc.html”
[92] “D_hypoleucum_27182_fastqc.zip”
[93] “D_hypoleucum_27450_fastqc.html”
[94] “D_hypoleucum_27450_fastqc.zip”
[95] “D_hypoleucum_27454_fastqc.html”
[96] “D_hypoleucum_27454_fastqc.zip”
[97] “D_hypoleucum_27468_fastqc.html”
[98] “D_hypoleucum_27468_fastqc.zip”
[99] “D_hypoleucum_27471_fastqc.html”
[100] “D_hypoleucum_27471_fastqc.zip”
[101] “D_hypoleucum_28273_fastqc.html”
[102] “D_hypoleucum_28273_fastqc.zip”
[103] “D_hypoleucum_28294_fastqc.html”
[104] “D_hypoleucum_28294_fastqc.zip”
[105] “D_hypoleucum_28329_fastqc.html”
[106] “D_hypoleucum_28329_fastqc.zip”
[107] “D_hypoleucum_28361_fastqc.html”
[108] “D_hypoleucum_28361_fastqc.zip”
[109] “D_hypoleucum_28376_fastqc.html”
[110] “D_hypoleucum_28376_fastqc.zip”
[111] “D_hypoleucum_28416_fastqc.html”
[112] “D_hypoleucum_28416_fastqc.zip”
[113] “D_hypoleucum_28584_fastqc.html”
[114] “D_hypoleucum_28584_fastqc.zip”
[115] “D_hypoleucum_28588_fastqc.html”
[116] “D_hypoleucum_28588_fastqc.zip”
[117] “D_hypoleucum_28596_fastqc.html”
[118] “D_hypoleucum_28596_fastqc.zip”
[119] “D_hypoleucum_28599_fastqc.html”
[120] “D_hypoleucum_28599_fastqc.zip”
[121] “D_hypoleucum_28663_fastqc.html”
[122] “D_hypoleucum_28663_fastqc.zip”
[123] “D_hypoleucum_28676_fastqc.html”
[124] “D_hypoleucum_28676_fastqc.zip”
[125] “D_hypoleucum_29945_fastqc.html”
[126] “D_hypoleucum_29945_fastqc.zip”
[127] “D_hypoleucum_29951_fastqc.html”
[128] “D_hypoleucum_29951_fastqc.zip”
[129] “D_hypoleucum_3095_fastqc.html”
[130] “D_hypoleucum_3095_fastqc.zip”
[131] “D_hypoleucum_3158_fastqc.html”
[132] “D_hypoleucum_3158_fastqc.zip”
[133] “D_hypoleucum_31636_fastqc.html”
[134] “D_hypoleucum_31636_fastqc.zip”
[135] “D_hypoleucum_31644_fastqc.html”
[136] “D_hypoleucum_31644_fastqc.zip”
[137] “D_hypoleucum_3208_fastqc.html”
[138] “D_hypoleucum_3208_fastqc.zip”
[139] “D_hypoleucum_3274_fastqc.html”
[140] “D_hypoleucum_3274_fastqc.zip”
[141] “D_hypoleucum_3275_fastqc.html”
[142] “D_hypoleucum_3275_fastqc.zip”
[143] “D_hypoleucum_3314_fastqc.html”
[144] “D_hypoleucum_3314_fastqc.zip”
[145] “D_hypoleucum_357608_fastqc.html”
[146] “D_hypoleucum_357608_fastqc.zip”
[147] “D_hypoleucum_357611_fastqc.html”
[148] “D_hypoleucum_357611_fastqc.zip”
[149] “D_hypoleucum_357612_fastqc.html”
[150] “D_hypoleucum_357612_fastqc.zip”
[151] “D_hypoleucum_357614_fastqc.html”
[152] “D_hypoleucum_357614_fastqc.zip”
[153] “D_hypoleucum_357615_fastqc.html”
[154] “D_hypoleucum_357615_fastqc.zip”
[155] “D_hypoleucum_454950_fastqc.html”
[156] “D_hypoleucum_454950_fastqc.zip”
[157] “D_hypoleucum_462070_fastqc.html”
[158] “D_hypoleucum_462070_fastqc.zip”
[159] “D_hypoleucum_472816_fastqc.html”
[160] “D_hypoleucum_472816_fastqc.zip”
[161] “D_hypoleucum_FMNH454949_fastqc.html” [162] “D_hypoleucum_FMNH454949_fastqc.zip” [163] “D_nigrilore_KU28413_fastqc.html”
[164] “D_nigrilore_KU28413_fastqc.zip”
[165] “D_nigrilore_KU28414_fastqc.html”
[166] “D_nigrilore_KU28414_fastqc.zip”
[167] “qc.Rmd”
[168] “run.fastqcr.sh”
[169] “slurm-39045614.out”
#create a character vector where each value is the full path to the .zip created by fastqc() for a given sample
samps<-list.files(qc.dir, full.names = T, pattern = "*.zip")
#plot qc test results for each sample
for (i in samps){
#read info for given sample from the .zip file generated in the previous step
samp.info <- qc_read(i)
#open blank list to hold qc visualizations for the given sample
plot<-list()
#do qc for the given sample
plot[[1]]<-qc_plot(samp.info, "Basic statistics")
plot[[2]]<-qc_plot(samp.info, "Per sequence quality scores")
plot[[3]]<-qc_plot(samp.info, "Sequence duplication levels")
#visualize tables
print(paste0("QC results for sample ", gsub(".*/", "", i)))
cat('\n')
print(kable(plot[[1]]))
cat('\n')
#visualize plots
grid.arrange(plot[[2]],plot[[3]],
ncol=2)
#clear plot to hold info for next sample
rm(plot)
}
[1] “QC results for sample D_hypoleucum_1271_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_1271.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 2562068 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample D_hypoleucum_1273_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_1273.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1078823 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 38 |
[1] “QC results for sample D_hypoleucum_1275_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_1275.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 10536603 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample D_hypoleucum_14037_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_14037.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 2022496 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample D_hypoleucum_14061_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_14061.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 4537 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample D_hypoleucum_14065_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_14065.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 2484741 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample D_hypoleucum_14075_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_14075.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 3086972 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample D_hypoleucum_14079_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_14079.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 429074 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample D_hypoleucum_14120_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_14120.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 181181 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample D_hypoleucum_14146_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_14146.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 121589 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample D_hypoleucum_14181_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_14181.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 2708992 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 38 |
[1] “QC results for sample D_hypoleucum_14225_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_14225.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 27815 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample D_hypoleucum_17969_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_17969.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 3739967 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample D_hypoleucum_17976_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_17976.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 128066 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample D_hypoleucum_18070_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_18070.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 662481 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample D_hypoleucum_18159_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_18159.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 2012398 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample D_hypoleucum_18188_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_18188.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 34854 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 38 |
[1] “QC results for sample D_hypoleucum_18191_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_18191.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1755921 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample D_hypoleucum_18193_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_18193.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 2319001 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 38 |
[1] “QC results for sample D_hypoleucum_19046_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_19046.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 4448354 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 38 |
[1] “QC results for sample D_hypoleucum_19066_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_19066.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 109819 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 36 |
[1] “QC results for sample D_hypoleucum_19136_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_19136.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 3442294 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 38 |
[1] “QC results for sample D_hypoleucum_19177_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_19177.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 786487 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample D_hypoleucum_19178_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_19178.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1164260 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample D_hypoleucum_1956_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_1956.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1126872 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 38 |
[1] “QC results for sample D_hypoleucum_19638_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_19638.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 575513 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample D_hypoleucum_20193_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_20193.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 149995 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 38 |
[1] “QC results for sample D_hypoleucum_20213_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_20213.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 263396 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 38 |
[1] “QC results for sample D_hypoleucum_20214_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_20214.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 5621 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 38 |
[1] “QC results for sample D_hypoleucum_20218_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_20218.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 3868526 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample D_hypoleucum_2067_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_2067.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1047026 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 38 |
[1] “QC results for sample D_hypoleucum_20921_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_20921.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1292366 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample D_hypoleucum_2208_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_2208.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1084240 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample D_hypoleucum_2229_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_2229.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 247956 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 38 |
[1] “QC results for sample D_hypoleucum_2253_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_2253.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 437506 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample D_hypoleucum_25622_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_25622.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 47472 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample D_hypoleucum_25637_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_25637.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1805728 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample D_hypoleucum_25670_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_25670.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 291600 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 38 |
[1] “QC results for sample D_hypoleucum_25672_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_25672.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 165351 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 38 |
[1] “QC results for sample D_hypoleucum_25675_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_25675.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 173293 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample D_hypoleucum_25868_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_25868.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 887902 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample D_hypoleucum_25880_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_25880.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 4183158 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample D_hypoleucum_25921_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_25921.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 3534392 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample D_hypoleucum_26975_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_26975.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 366479 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 38 |
[1] “QC results for sample D_hypoleucum_26984_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_26984.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1512918 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample D_hypoleucum_27182_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_27182.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 67266 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample D_hypoleucum_27450_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_27450.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 890749 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample D_hypoleucum_27454_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_27454.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 26782 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample D_hypoleucum_27468_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_27468.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 28673 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample D_hypoleucum_27471_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_27471.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 50538 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 38 |
[1] “QC results for sample D_hypoleucum_28273_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_28273.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 12893 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample D_hypoleucum_28294_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_28294.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 7237647 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 38 |
[1] “QC results for sample D_hypoleucum_28329_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_28329.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 728838 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 38 |
[1] “QC results for sample D_hypoleucum_28361_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_28361.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 6004872 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 38 |
[1] “QC results for sample D_hypoleucum_28376_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_28376.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 4319704 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample D_hypoleucum_28416_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_28416.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 2567648 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 38 |
[1] “QC results for sample D_hypoleucum_28584_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_28584.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 6512 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 36 |
[1] “QC results for sample D_hypoleucum_28588_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_28588.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 33935 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 38 |
[1] “QC results for sample D_hypoleucum_28596_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_28596.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 26278 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample D_hypoleucum_28599_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_28599.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 32074 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample D_hypoleucum_28663_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_28663.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 5416453 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 39 |
[1] “QC results for sample D_hypoleucum_28676_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_28676.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 2472283 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 38 |
[1] “QC results for sample D_hypoleucum_29945_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_29945.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1487775 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 38 |
[1] “QC results for sample D_hypoleucum_29951_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_29951.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 3440054 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 38 |
[1] “QC results for sample D_hypoleucum_3095_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_3095.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 579001 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample D_hypoleucum_3158_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_3158.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1092329 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample D_hypoleucum_31636_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_31636.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1612710 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 38 |
[1] “QC results for sample D_hypoleucum_31644_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_31644.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 785653 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 38 |
[1] “QC results for sample D_hypoleucum_3208_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_3208.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1499320 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 38 |
[1] “QC results for sample D_hypoleucum_3274_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_3274.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 4454397 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample D_hypoleucum_3275_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_3275.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 7125 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 35 |
[1] “QC results for sample D_hypoleucum_3314_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_3314.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 922902 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 38 |
[1] “QC results for sample D_hypoleucum_357608_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_357608.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 159823 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample D_hypoleucum_357611_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_357611.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 785 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 39 |
[1] “QC results for sample D_hypoleucum_357612_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_357612.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 150533 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample D_hypoleucum_357614_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_357614.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 21079 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample D_hypoleucum_357615_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_357615.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1541338 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample D_hypoleucum_454950_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_454950.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 974035 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample D_hypoleucum_462070_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_462070.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 2014875 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample D_hypoleucum_472816_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_472816.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 3994 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 36 |
[1] “QC results for sample D_hypoleucum_FMNH454949_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_hypoleucum_FMNH454949.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 263252 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample D_nigrilore_KU28413_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_nigrilore_KU28413.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 696250 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 38 |
[1] “QC results for sample D_nigrilore_KU28414_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | D_nigrilore_KU28414.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 2225205 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 38 |
#aggregate the reports by pointing this function to the folder holding output of fastqc()
qc <- qc_aggregate(qc.dir, progressbar = F)
#stats per sample
knitr::kable(qc_stats(qc))
| sample | pct.dup | pct.gc | tot.seq | seq.length |
|---|---|---|---|---|
| D_hypoleucum_1271.fq.gz | 96.84 | 37 | 2562068 | 95 |
| D_hypoleucum_1273.fq.gz | 95.72 | 38 | 1078823 | 95 |
| D_hypoleucum_1275.fq.gz | 97.85 | 37 | 10536603 | 95 |
| D_hypoleucum_14037.fq.gz | 96.27 | 37 | 2022496 | 95 |
| D_hypoleucum_14061.fq.gz | 53.36 | 37 | 4537 | 95 |
| D_hypoleucum_14065.fq.gz | 96.78 | 37 | 2484741 | 95 |
| D_hypoleucum_14075.fq.gz | 96.95 | 37 | 3086972 | 95 |
| D_hypoleucum_14079.fq.gz | 92.98 | 37 | 429074 | 95 |
| D_hypoleucum_14120.fq.gz | 89.20 | 37 | 181181 | 95 |
| D_hypoleucum_14146.fq.gz | 87.90 | 37 | 121589 | 95 |
| D_hypoleucum_14181.fq.gz | 96.44 | 38 | 2708992 | 95 |
| D_hypoleucum_14225.fq.gz | 74.61 | 37 | 27815 | 95 |
| D_hypoleucum_17969.fq.gz | 97.20 | 37 | 3739967 | 95 |
| D_hypoleucum_17976.fq.gz | 88.83 | 37 | 128066 | 95 |
| D_hypoleucum_18070.fq.gz | 94.38 | 37 | 662481 | 95 |
| D_hypoleucum_18159.fq.gz | 96.98 | 37 | 2012398 | 95 |
| D_hypoleucum_18188.fq.gz | 79.26 | 38 | 34854 | 95 |
| D_hypoleucum_18191.fq.gz | 96.92 | 37 | 1755921 | 95 |
| D_hypoleucum_18193.fq.gz | 96.87 | 38 | 2319001 | 95 |
| D_hypoleucum_19046.fq.gz | 97.12 | 38 | 4448354 | 95 |
| D_hypoleucum_19066.fq.gz | 87.88 | 36 | 109819 | 95 |
| D_hypoleucum_19136.fq.gz | 97.33 | 38 | 3442294 | 95 |
| D_hypoleucum_19177.fq.gz | 95.29 | 37 | 786487 | 95 |
| D_hypoleucum_19178.fq.gz | 96.26 | 37 | 1164260 | 95 |
| D_hypoleucum_1956.fq.gz | 95.40 | 38 | 1126872 | 95 |
| D_hypoleucum_19638.fq.gz | 94.78 | 37 | 575513 | 95 |
| D_hypoleucum_20193.fq.gz | 87.89 | 38 | 149995 | 95 |
| D_hypoleucum_20213.fq.gz | 92.61 | 38 | 263396 | 95 |
| D_hypoleucum_20214.fq.gz | 70.36 | 38 | 5621 | 95 |
| D_hypoleucum_20218.fq.gz | 97.54 | 37 | 3868526 | 95 |
| D_hypoleucum_2067.fq.gz | 95.20 | 38 | 1047026 | 95 |
| D_hypoleucum_20921.fq.gz | 95.50 | 37 | 1292366 | 95 |
| D_hypoleucum_2208.fq.gz | 95.43 | 37 | 1084240 | 95 |
| D_hypoleucum_2229.fq.gz | 83.50 | 38 | 247956 | 95 |
| D_hypoleucum_2253.fq.gz | 93.87 | 37 | 437506 | 95 |
| D_hypoleucum_25622.fq.gz | 82.51 | 37 | 47472 | 95 |
| D_hypoleucum_25637.fq.gz | 95.75 | 37 | 1805728 | 95 |
| D_hypoleucum_25670.fq.gz | 91.11 | 38 | 291600 | 95 |
| D_hypoleucum_25672.fq.gz | 87.82 | 38 | 165351 | 95 |
| D_hypoleucum_25675.fq.gz | 90.30 | 37 | 173293 | 95 |
| D_hypoleucum_25868.fq.gz | 94.59 | 37 | 887902 | 95 |
| D_hypoleucum_25880.fq.gz | 97.45 | 37 | 4183158 | 95 |
| D_hypoleucum_25921.fq.gz | 97.01 | 37 | 3534392 | 95 |
| D_hypoleucum_26975.fq.gz | 91.13 | 38 | 366479 | 95 |
| D_hypoleucum_26984.fq.gz | 96.09 | 37 | 1512918 | 95 |
| D_hypoleucum_27182.fq.gz | 84.92 | 37 | 67266 | 95 |
| D_hypoleucum_27450.fq.gz | 94.08 | 37 | 890749 | 95 |
| D_hypoleucum_27454.fq.gz | 73.99 | 37 | 26782 | 95 |
| D_hypoleucum_27468.fq.gz | 65.15 | 37 | 28673 | 95 |
| D_hypoleucum_27471.fq.gz | 79.26 | 38 | 50538 | 95 |
| D_hypoleucum_28273.fq.gz | 68.49 | 37 | 12893 | 95 |
| D_hypoleucum_28294.fq.gz | 97.61 | 38 | 7237647 | 95 |
| D_hypoleucum_28329.fq.gz | 94.23 | 38 | 728838 | 95 |
| D_hypoleucum_28361.fq.gz | 97.55 | 38 | 6004872 | 95 |
| D_hypoleucum_28376.fq.gz | 97.21 | 37 | 4319704 | 95 |
| D_hypoleucum_28416.fq.gz | 96.84 | 38 | 2567648 | 95 |
| D_hypoleucum_28584.fq.gz | 77.21 | 36 | 6512 | 95 |
| D_hypoleucum_28588.fq.gz | 75.69 | 38 | 33935 | 95 |
| D_hypoleucum_28596.fq.gz | 75.04 | 37 | 26278 | 95 |
| D_hypoleucum_28599.fq.gz | 69.27 | 37 | 32074 | 95 |
| D_hypoleucum_28663.fq.gz | 97.71 | 39 | 5416453 | 95 |
| D_hypoleucum_28676.fq.gz | 96.87 | 38 | 2472283 | 95 |
| D_hypoleucum_29945.fq.gz | 95.94 | 38 | 1487775 | 95 |
| D_hypoleucum_29951.fq.gz | 97.37 | 38 | 3440054 | 95 |
| D_hypoleucum_3095.fq.gz | 94.59 | 37 | 579001 | 95 |
| D_hypoleucum_3158.fq.gz | 96.00 | 37 | 1092329 | 95 |
| D_hypoleucum_31636.fq.gz | 95.67 | 38 | 1612710 | 95 |
| D_hypoleucum_31644.fq.gz | 94.85 | 38 | 785653 | 95 |
| D_hypoleucum_3208.fq.gz | 96.53 | 38 | 1499320 | 95 |
| D_hypoleucum_3274.fq.gz | 97.49 | 37 | 4454397 | 95 |
| D_hypoleucum_3275.fq.gz | 79.69 | 35 | 7125 | 95 |
| D_hypoleucum_3314.fq.gz | 95.93 | 38 | 922902 | 95 |
| D_hypoleucum_357608.fq.gz | 88.82 | 37 | 159823 | 95 |
| D_hypoleucum_357611.fq.gz | 77.32 | 39 | 785 | 95 |
| D_hypoleucum_357612.fq.gz | 90.21 | 37 | 150533 | 95 |
| D_hypoleucum_357614.fq.gz | 68.76 | 37 | 21079 | 95 |
| D_hypoleucum_357615.fq.gz | 96.66 | 37 | 1541338 | 95 |
| D_hypoleucum_454950.fq.gz | 95.81 | 37 | 974035 | 95 |
| D_hypoleucum_462070.fq.gz | 96.78 | 37 | 2014875 | 95 |
| D_hypoleucum_472816.fq.gz | 76.74 | 36 | 3994 | 95 |
| D_hypoleucum_FMNH454949.fq.gz | 89.17 | 37 | 263252 | 95 |
| D_nigrilore_KU28413.fq.gz | 94.49 | 38 | 696250 | 95 |
| D_nigrilore_KU28414.fq.gz | 96.26 | 38 | 2225205 | 95 |
#save stats info as an object
stats.info<-qc_stats(qc)
#make tot.seq numeric
stats.info$tot.seq<-as.numeric(stats.info$tot.seq)
#make histogram of number of sequence reads for each sample
ggplot(stats.info, aes(x=tot.seq))+
geom_histogram(color="black", fill="white", bins=20)+
geom_vline(aes(xintercept=median(tot.seq)), color = "red")+
geom_vline(aes(xintercept=median(tot.seq)*.1), color = "red", lty=14)+
theme_classic()+
xlab("Number of sequencing reads")
#solid red line = median sample value
#dashed red line = 10% of median sample value
ggplot(stats.info, aes(x=tot.seq))+
geom_histogram(color="black", fill="white", bins=200)+
geom_vline(aes(xintercept=median(tot.seq)), color = "red")+
geom_vline(aes(xintercept=median(tot.seq)*.1), color = "red", lty=14)+
theme_classic()+
xlab("Number of sequencing reads")
#show me the samples that have less than 10% of the number of reads as the median sample from this experiment (these should be dropped immediately)
print(paste("Median sample contains", median(stats.info$tot.seq), "reads. The following samples contain less than", median(stats.info$tot.seq)*.1, "reads (10% of the median), and should likely be dropped"))
[1] “Median sample contains 887902 reads. The following samples contain less than 88790.2 reads (10% of the median), and should likely be dropped”
knitr::kable(stats.info[stats.info$tot.seq < median(stats.info$tot.seq)*.1,])
| sample | pct.dup | pct.gc | tot.seq | seq.length |
|---|---|---|---|---|
| D_hypoleucum_14061.fq.gz | 53.36 | 37 | 4537 | 95 |
| D_hypoleucum_14225.fq.gz | 74.61 | 37 | 27815 | 95 |
| D_hypoleucum_18188.fq.gz | 79.26 | 38 | 34854 | 95 |
| D_hypoleucum_20214.fq.gz | 70.36 | 38 | 5621 | 95 |
| D_hypoleucum_25622.fq.gz | 82.51 | 37 | 47472 | 95 |
| D_hypoleucum_27182.fq.gz | 84.92 | 37 | 67266 | 95 |
| D_hypoleucum_27454.fq.gz | 73.99 | 37 | 26782 | 95 |
| D_hypoleucum_27468.fq.gz | 65.15 | 37 | 28673 | 95 |
| D_hypoleucum_27471.fq.gz | 79.26 | 38 | 50538 | 95 |
| D_hypoleucum_28273.fq.gz | 68.49 | 37 | 12893 | 95 |
| D_hypoleucum_28584.fq.gz | 77.21 | 36 | 6512 | 95 |
| D_hypoleucum_28588.fq.gz | 75.69 | 38 | 33935 | 95 |
| D_hypoleucum_28596.fq.gz | 75.04 | 37 | 26278 | 95 |
| D_hypoleucum_28599.fq.gz | 69.27 | 37 | 32074 | 95 |
| D_hypoleucum_3275.fq.gz | 79.69 | 35 | 7125 | 95 |
| D_hypoleucum_357611.fq.gz | 77.32 | 39 | 785 | 95 |
| D_hypoleucum_357614.fq.gz | 68.76 | 37 | 21079 | 95 |
| D_hypoleucum_472816.fq.gz | 76.74 | 36 | 3994 | 95 |